Eutrophication of freshwaters occurs in watersheds with excessive pollution of phosphorus (P). Factors that affect P cycling and transport, including climate and land use, are changing rapidly and can have legacy effects, making future freshwater quality uncertain. Focusing on the Yahara Watershed (YW) of southern Wisconsin, USA, an intensive agricultural landscape, we explored the relative influence of land use and climate on three indicators of water quality over a span of 57 years (2014–2070). The indicators included watershed-averaged P yield from the land surface, direct drainage P loads to a lake, and average summertime lake P concentration. Using biophysical model simulations of future watershed scenarios, we found that climate exerted a stronger influence than land use on all three indicators, yet land use had an important role in influencing long term outcomes for each. Variations in P yield due to land use exceeded those due to climate in 36 of 57 years, whereas variations in load and lake total P concentration due to climate exceeded those due to land use in 54 of 57 years, and 52 of 57 years, respectively. The effect of land use was thus strongest for P yield off the landscape and attenuated in the stream and lake aquatic systems where the influence of weather variability was greater. Overall these findings underscore the dominant role of climate in driving inter-annual nutrient fluxes within the hydrologic network and suggest a challenge for land use to influence water quality within streams and lakes over timescales less than a decade. Over longer timescales, reducing applications of P throughout the watershed was an effective management strategy under all four climates investigated, even during decades with wetter conditions and more frequent extreme precipitation events.